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From 10/31/2016 to 11/29/2016

11/29/2016

06:01 PM Revision 5a079dbf (cdm-dataportal): ref #2985 units in min max measures only at the end and after...
Andreas Kohlbecker
06:00 PM feature request #2985 (In Progress): Improve Specimen details display
Andreas Kohlbecker
05:42 PM Revision 17e693bd (cdmlib-apps): Avoid cloning taxa for checklist classification
Patrick Plitzner
05:17 PM bug #6227 (Closed): LIE during request to derivedUnitFacade/{uuid}/collectingareas
http://api.cybertaxonomy.org:80/flora_central_africa/derivedUnitFacade/70c3540a-fefb-4152-9dbf-aef1ae5ffff9/collectin... Andreas Kohlbecker
04:42 PM bug #3061 (Closed): Lecototype typeReference not rendered correctly
test are running successful and are thus confirming the expectations. Ticket fully solved Andreas Kohlbecker
04:41 PM bug #3061 (Resolved): Lecototype typeReference not rendered correctly
Andreas Kohlbecker
04:36 PM Revision 3a3d658d (cdm-dataportal): ref #3061 adapting test and test data
Andreas Kohlbecker
03:46 PM Revision c7f92453 (cdm-dataportal): ref #3061 using the full publication timePeriod instead of on...
Andreas Kohlbecker
03:30 PM Revision c5294246 (cdm-dataportal): ref #3061 fixing position of footnote
Andreas Kohlbecker
01:30 PM Revision 6fac16b9 (cdmlib-apps): Removed all occurrences of "checklist" related code
Patrick Plitzner
12:25 PM Revision b0269b24 (cdm-dataportal): ref #3061 removing cluetip js which is no longer used
Andreas Kohlbecker
11:33 AM bug #6199: Excluded note for excluded taxon nodes in TaxEdtior
I could only reproduce the strange behavior (TaxonNode excluded and unplaced flag not initialised) in one data source... Patrick Plitzner
11:28 AM Revision dbd15c7d (cdmlib-apps): Adapt SQL queries to filter for only Buttler approved taxa
Patrick Plitzner

11/28/2016

06:41 PM bug #5938 (Closed): distribution and specimen maps can not be used on the same page
Andreas Kohlbecker
01:39 PM bug #5938 (Resolved): distribution and specimen maps can not be used on the same page
Applied in changeset commit:cdm-dataportal|669f08ee073432d163976f10b59f1d516e71f827. Andreas Kohlbecker
01:23 PM bug #5938 (In Progress): distribution and specimen maps can not be used on the same page
Andreas Kohlbecker
06:38 PM feature request #3650 (Closed): allow supressing empty distribution and specimen maps
Andreas Kohlbecker
05:35 PM feature request #3650 (Resolved): allow supressing empty distribution and specimen maps
Applied in changeset commit:cdm-dataportal|378bc1ce4c8e704cde2fc41d11ab4f81b3b2275d. Andreas Kohlbecker
04:25 PM feature request #3650 (In Progress): allow supressing empty distribution and specimen maps
Andreas Kohlbecker
06:38 PM Revision e0613197 (cdm-dataportal): fix #3650 visibility of distribution and specimen maps config...
Andreas Kohlbecker
05:34 PM Revision 378bc1ce (cdm-dataportal): fix #3650 visibility of distribution and specimen maps config...
Andreas Kohlbecker
04:24 PM feature request #5047 (Duplicate): option to show empty distribution maps
Andreas Kohlbecker
01:40 PM task #6226: Delete orphaned key nodes
~~~ sql
SELECT *
FROM PolytomousKeyNode pkn
WHERE pkn.key_id NOT IN (SELECT id FROM PolytomousKey);
~~~
Andreas Müller
01:39 PM task #6226 (Closed): Delete orphaned key nodes
As deletion did not work correctly for long time we do still have PolytomousKeyNodes that do reference a PolytomousKe... Andreas Müller
01:39 PM Revision 669f08ee (cdm-dataportal): fix #5938 unique ids for each openlayers block elements
Andreas Kohlbecker
01:24 PM Revision 4c21ffdb (cdm-dataportal): ref #5938 fixing js lib loading order (and defined map contai...
Andreas Kohlbecker
01:23 PM feature request #6225 (New): Allow to freeze referencing objects view
Sometimes one wants to check some of the referencing objects by navigating to them without loosing the list. This is ... Andreas Müller
12:40 PM Revision 653e9c6b (cdm-dataportal): maps documentation, refactoring of unused params etc, unique ...
Andreas Kohlbecker
11:43 AM Revision f4675ec1 (cdm-dataportal): doc minor
Andreas Kohlbecker
10:31 AM feature request #5844 (Closed): Make stable identifier clickable in default specimen tab
Andreas Kohlbecker
10:30 AM feature request #5844 (Resolved): Make stable identifier clickable in default specimen tab
Applied in changeset commit:cdm-dataportal|a9ed34adc02e785439264eca051e15954bdeb72c. Andreas Kohlbecker
10:30 AM Revision a9ed34ad (cdm-dataportal): fix #5844 persistent stable identifier clickable
- clickable in specimen tab
- implementation harmonized in specimen table ref #5515
Andreas Kohlbecker
08:34 AM bug #6211 (Closed): massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
I agree! Andreas Kohlbecker

11/27/2016

10:42 AM bug #6211: massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
Both examples do now have < 1MB and load in reasonable time <= 5 sec. There still might be possibilities to improve t... Andreas Müller

11/25/2016

08:05 PM bug #6190: remove svn property place holder in first line of code
This can now be done automatically as model changes are fully merged into develop now. Andreas Müller
06:18 PM bug #6224 (Resolved): cdm-webapp is not using current version of cdmlib-remote-webapp.war
Applied in changeset commit:cdm-webapp|f55d498166acfa645e4f31af5869302f6acdb814. Andreas Kohlbecker
06:09 PM bug #6224 (In Progress): cdm-webapp is not using current version of cdmlib-remote-webapp.war
Andreas Kohlbecker
05:40 PM bug #6224 (Closed): cdm-webapp is not using current version of cdmlib-remote-webapp.war
After pushing a specific commit to the server and runing the build pipeline the resulting cdm-server is nor making u... Andreas Kohlbecker
06:15 PM Revision f55d4981 (cdm-webapp): fix #6224 swapping the war overlay order to avoid build pipeline ...
Andreas Kohlbecker
05:23 PM Revision 484bf7ea (cdmlib): ref #6211 cleanup old code
Andreas Müller
05:22 PM Revision 71b8be7f (cdmlib): cleanup
Andreas Müller
05:21 PM bug #6122 (Resolved): add titleCache service
Applied in changeset commit:cdmlib|b3a692b2ee3c7d7a5305a0b9901eaefcc87ca8f7. Andreas Müller
05:21 PM Revision b3a692b2 (cdmlib): fix #6122 use StringResultDTO for titleCache service
Andreas Müller
04:42 PM Revision 0245ae20 (cdmlib): doc
Andreas Müller
03:44 PM bug #6223 (New): change behaviour of AbstractBeanProcessor.excludes to asReference
With the excludes property the AbstractBeanProcessor provides a means to omit specific CDM-Bean properties from being... Andreas Kohlbecker
03:42 PM Revision be11c810 (cdmlib): cleanup
Andreas Müller
03:40 PM bug #6220: Improve definition of orphaned taxon and synonym
Andreas Müller wrote:
> Katja Luther wrote:
> > The open in works correctly now. The wrong symbol for taxa with con...
Katja Luther
03:35 PM bug #6220: Improve definition of orphaned taxon and synonym
Katja Luther wrote:
> The open in works correctly now. The wrong symbol for taxa with conceptrelationships/misapplie...
Andreas Müller
01:15 PM bug #6220: Improve definition of orphaned taxon and synonym
Andreas Müller wrote:
> Katja Luther wrote:
> > Andreas Müller wrote:
> > > The fix works so far that search resul...
Katja Luther
12:01 PM bug #6220: Improve definition of orphaned taxon and synonym
Katja Luther wrote:
> Andreas Müller wrote:

> > Also orphaned synonyms are not found in TaxEditor taxon bulk edi...
Andreas Müller
11:55 AM bug #6220: Improve definition of orphaned taxon and synonym
Katja Luther wrote:
> Andreas Müller wrote:
> > The fix works so far that search result in TaxEditor allow only ope...
Andreas Müller
11:44 AM bug #6220: Improve definition of orphaned taxon and synonym
Andreas Müller wrote:
> The fix works so far that search result in TaxEditor allow only opening in TaxEditor now. Ho...
Katja Luther
03:37 PM task #6208 (Rejected): implement synonymy service responding with DTO
The fixes for #6211 improve the situation tremendously. Implementing a pure DTO may be a complex task therefore we re... Andreas Müller
03:25 PM bug #6201 (Closed): Adapt dataportal to the new synonym datamodel
I guess it is all ok. Andreas Müller
12:01 PM bug #6201 (Resolved): Adapt dataportal to the new synonym datamodel
ready for review if needed. Otherwise the synonymy is quite good covered by tests and can be considered to be ok sinc... Andreas Kohlbecker
03:08 PM feature request #6216 (Closed): Allow changing of defaultColor for PresenceAbsenceTerm
Looks good Andreas Müller
03:05 PM Revision 0ede0320 (cdmlib): ref #6211 avoiding to deep initialization of synonym groups
Andreas Kohlbecker
02:11 PM bug #6210 (Closed): Null values for boolean fields are causing PropertyAccessException
this is working now! Andreas Kohlbecker
01:48 PM bug #3226: openlayers map google baselayers: api keys rejected
Hi Gabi,
please can you do the review for this ticket? This it as brief how-to:
1. got to http://test.e-taxonom...
Andreas Kohlbecker
01:43 PM bug #3226 (Resolved): openlayers map google baselayers: api keys rejected
Applied in changeset commit:cdm-dataportal|2b83cc8b859c5bfa6ffb07ccc9c090f3031c6f1a. Andreas Kohlbecker
01:42 PM bug #3226 (In Progress): openlayers map google baselayers: api keys rejected
Andreas Kohlbecker
01:46 PM Revision f619ffbf (cdm-dataportal): openlayers maps cleaning up
Andreas Kohlbecker
01:43 PM bug #6211 (Resolved): massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
Applied in changeset commit:cdmlib|17b0c5e7b5ebc5dbe384f62928c3b394d5bb9ece. Andreas Müller
07:08 AM bug #6211: massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
Alternatively we may check if it is possible to adapt getSynonymsByHomotypicGroup() such that less data is initialized. Andreas Müller
06:39 AM bug #6211: massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
The reason for this problem is, that the TaxonPortalController calls the ITaxonService.getSynonymsByHomotypicGroup() ... Andreas Müller
01:42 PM Revision 2b83cc8b (cdm-dataportal): fix #3226 fixing broken Google map layers
Andreas Kohlbecker
01:39 PM Revision 11aa2415 (cdmlib): fix #6211 fix API incompatibility
Andreas Müller
01:08 PM Revision d11d4dd0 (cdmlib): cleanup
Andreas Müller
01:05 PM Revision 17b0c5e7 (cdmlib): fix #6211 reduce initialization for synonymy
Andreas Müller
12:59 PM Revision a6de10b5 (taxeditor): ref #6219: add warning that synonym is deleted immediately
Katja Luther
11:53 AM Revision f06c2616 (cdm-dataportal): ref #6222 adding ticket reference to comment
Andreas Kohlbecker
11:52 AM bug #6222 (New): harmonize classification service return types for the data portal
there is one service request which not yet returning TaxonNodeTDO object, this can cause problems in rare cases.
...
Andreas Kohlbecker
11:44 AM task #6221 (New): mention the unplaced and excluded states in the taxon page
Taxon nodes can be flagged with unplaced and excluded should this be mentioned in the portal page and how should it b... Andreas Kohlbecker
11:39 AM feature request #6203: Implement unplaced and excluded in dataportal
unplaced and excluded are handled correctly in the portal at least in the sense that the model change is not causing ... Andreas Kohlbecker
11:20 AM Revision a0e3ae5c (cdm-dataportal): ref #6203 checked return types of classification services and...
Andreas Kohlbecker
09:45 AM bug #6219: Deleting synonym is persisted immediately, but the editor is set dirty
I think it would be nice to implement it in a way similar to the bulkeditor, therefore we have to reconstruct the nam... Katja Luther
09:01 AM bug #6219: Deleting synonym is persisted immediately, but the editor is set dirty
The preferred solution is to handle it similar to bulk editor where the deletion from database is invoked only with s... Andreas Müller

11/24/2016

04:35 PM Revision 58525579 (cdmlib): ref #6211 try to fix heap consumption in synonymy service
Andreas Müller
04:31 PM Revision ed27e451 (cdmlib): minor
Andreas Müller
02:50 PM Revision ab94d85b (taxeditor): l10n for PresenceAbsenceTermDetailElement
Patrick Plitzner
02:33 PM feature request #6203: Implement unplaced and excluded in dataportal
Katja, could you have a look on this.
We definetely need to move the unplaced and excluded (in this order) taxa to...
Andreas Müller
02:27 PM Revision cb1498ea (taxeditor): ref #6216 Added button to select color instead of clicking on color
field
- resized color field
Patrick Plitzner
02:27 PM Revision 3dbe4420 (taxeditor): Align label to the middle
Patrick Plitzner
02:24 PM feature request #5616: Add the"Open in..." menu to taxon search
4b80789a fixed the "Open in ..." issue. However there are open questions related to orphaned taxa. See #6220. Andreas Müller
01:34 PM feature request #5616: Add the"Open in..." menu to taxon search
Katja Luther wrote:
> The problem seems to be in the calculation of the orphan value. A taxon is only orphaned when ...
Andreas Müller
02:21 PM bug #6220 (Feedback): Improve definition of orphaned taxon and synonym
The fix works so far that search result in TaxEditor allow only opening in TaxEditor now. However, an orphaned taxon ... Andreas Müller
01:35 PM bug #6220 (Resolved): Improve definition of orphaned taxon and synonym
Applied in changeset commit:cdmlib|4b80789a6d183956c922de22091164555d2ef442. Andreas Müller
01:32 PM bug #6220 (Feedback): Improve definition of orphaned taxon and synonym
Currently taxa are only orphaned if they have no taxon node AND no concept relationships. The later is critical as ta... Andreas Müller
01:44 PM Revision c6c4ab3a (cdmlib): ref #6220 javadoc
Andreas Müller
01:43 PM bug #4945 (Resolved): Right click menu for polytomous key node list view needs correct enabling
Katja Luther
01:42 PM bug #4945 (New): Right click menu for polytomous key node list view needs correct enabling
Katja Luther
01:42 PM bug #4945 (Resolved): Right click menu for polytomous key node list view needs correct enabling
Applied in changeset commit:taxeditor|f81dda1f2c57e7a51be26ab87b68bebda8d0fee4. Katja Luther
01:41 PM Revision f81dda1f (taxeditor): fix #4945: add propertytester for polytomouskeynode to enable menu...
Katja Luther
01:39 PM feature request #5971 (Resolved): Implement database wide CdmPreference writing
Applied in changeset commit:taxeditor|bb920fa17ba6147e45ad67cc651c703584cdcbd6. Katja Luther
01:39 PM Revision bb920fa1 (taxeditor): fix #5971: move admin menu in front of Help
Katja Luther
01:33 PM Revision 4b80789a (cdmlib): fix #6220 Improve isOrphaned definition for Taxon.
Andreas Müller
01:18 PM bug #6219 (Closed): Deleting synonym is persisted immediately, but the editor is set dirty
When deleting a synonym in name editor the deletion is persisted immediately. The editor is set dirty that looks like... Katja Luther
12:37 PM bug #5693 (Closed): Deleting a synonym only deletes the synonym relation
This seems to be fixed also after model changes (removed synonym relationship class). However there are issues about ... Andreas Müller
12:23 PM feature request #6198 (Closed): Remove synonym relationships in TaxEditor
Andreas Müller
12:18 PM Revision 0908acf3 (taxeditor): Adapt labels for taxon node agent relation editing
Andreas Müller
12:03 PM bug #6199: Excluded note for excluded taxon nodes in TaxEdtior
Patrick Plitzner wrote:
> Patrick Plitzner wrote:
> > While reviewing I saw that even the isExcluded is not persist...
Andreas Müller
12:00 PM Revision f83def50 (cdmlib): ref #6199 test for reading excluded, unplaced and excludedNote
Andreas Müller
11:16 AM bug #6218 (Closed): NPE when editing term vocabulary label
When trying to edit the label of a new vocabulary (PresenceAbsenceTerm) I got the below NPE.
I think it happened wh...
Andreas Müller
11:08 AM bug #6217: Adapt colour mapping in dataportals
Projects that might want to use the feature are Caucasus and Asteracea which do have or plan to have multiple data po... Andreas Müller
11:06 AM bug #6217 (New): Adapt colour mapping in dataportals
Currently there is the possibility to adapt the color of a PresenceAbsenceTerm in a distribution map by using the acc... Andreas Müller
10:58 AM feature request #6216 (Feedback): Allow changing of defaultColor for PresenceAbsenceTerm
Works well and ticket can be closed. Only issues might be layout issues:
1. Personally I find it better to have a ...
Andreas Müller
10:23 AM feature request #6216 (Resolved): Allow changing of defaultColor for PresenceAbsenceTerm
Applied in changeset commit:taxeditor|cf4bd11fd2a394c795f744111f8b2cbf7f59f7e5. Patrick Plitzner
10:21 AM feature request #6216 (Closed): Allow changing of defaultColor for PresenceAbsenceTerm
Patrick Plitzner
10:25 AM Revision 15f5a1bd (taxeditor): ref #6216 Pre-select color in ColorDialog
Patrick Plitzner
10:24 AM Revision 20718782 (cdmlib-apps): ref #3934 update Salvador import for facts
Andreas Müller
10:22 AM Revision cf4bd11f (taxeditor): fix #6216 Implement color dialog to change color of presence absence
terms Patrick Plitzner
09:52 AM Revision 033aad78 (taxeditor): all polytomouskey related handler are now extended from RemotingCd...
Katja Luther

11/23/2016

05:01 PM bug #6199: Excluded note for excluded taxon nodes in TaxEdtior
Patrick Plitzner wrote:
> While reviewing I saw that even the isExcluded is not persisted anymore. Have to recheck i...
Patrick Plitzner
04:19 PM bug #6199: Excluded note for excluded taxon nodes in TaxEdtior
While reviewing I saw that even the isExcluded is not persisted anymore. Have to recheck if anything has changed Patrick Plitzner
04:11 PM bug #6211: massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
This seems to be caused by a cycle in the object graph which is either not detected or not handled correctly by json-... Andreas Kohlbecker
03:54 PM bug #6210: Null values for boolean fields are causing PropertyAccessException
This is still occurring for me:
* database restored from dump: cdm_integration_cichorieae_2016-11-10_06h25m.Thursd...
Andreas Kohlbecker
02:11 PM bug #6210 (Resolved): Null values for boolean fields are causing PropertyAccessException
Fixed with f3d4c9bc Andreas Müller
03:45 PM bug #6206 (Closed): Vaadin view fail with: Failed to load the bootstrap javascript
Vaadin works on the test server. Seems fine. Patrick Plitzner
03:04 PM feature request #5841 (Resolved): Creating a new alternative in PolytomousKey Editor should set f...
Applied in changeset commit:taxeditor|efd30f4b550d4e53206d2c5d5a720381a5663611. Katja Luther
03:04 PM Revision efd30f4b (taxeditor): fix #5841: set selection to newly created keynode
Katja Luther
02:55 PM bug #6215 (Resolved): NPE when opening preferences with no DB connection
Applied in changeset commit:taxeditor|84ab8cb061709145c824967aa8a3a10742e875ff. Katja Luther
02:38 PM bug #6215 (Closed): NPE when opening preferences with no DB connection
When trying to open the preferences for all "Taxonomic Editor"-"Taxonomic" submenus an NPE is thrown.
~~~
l...
Andreas Müller
02:54 PM Revision 84ab8cb0 (taxeditor): fix #6215: check for datasource when opening preferencepage
Katja Luther
02:41 PM feature request #5971 (Feedback): Implement database wide CdmPreference writing
Andreas Müller
02:41 PM feature request #5971: Implement database wide CdmPreference writing
Please move the new menu in between Extras/Window and Help. Help should always be the last in the row. Andreas Müller
10:26 AM feature request #5971 (Resolved): Implement database wide CdmPreference writing
Applied in changeset commit:taxeditor|0bd095d9fbccd25ce847af780892633284b314f9. Katja Luther
09:29 AM feature request #5971: Implement database wide CdmPreference writing
Now we have a main menu admin. This menu should only be visible for admins or project manager. Katja Luther
02:27 PM feature request #5969 (Closed): Implement CdmPreference reading for database preferences
I think we can close this ticket now. Open issues will be checked in #5971 and are more related to writing then reading Andreas Müller
02:11 PM feature request #6203: Implement unplaced and excluded in dataportal
> Unplaced taxon nodes should be put to an incertis sedis node in the tree. Excluded nodes should be put to an exclud... Andreas Kohlbecker
01:20 PM Revision f3d4c9bc (cdmlib): Fix proparte is null in update script
Andreas Müller
01:19 PM Revision c1bd6833 (cdmlib): cleanup
Andreas Müller
11:15 AM bug #6214 (Closed): Add project specific preferences to CdmPreference menu
For now we have two project specific preferences: RedList (EditorProfile->Rote Liste 2020) and Campanula (Specimens a... Patrick Plitzner
10:33 AM bug #6105 (Resolved): Make CdmPreferences editable in separate view
Katja Luther
10:32 AM bug #6105: Make CdmPreferences editable in separate view
This is done, see #5971 Katja Luther
10:22 AM Revision 0bd095d9 (taxeditor): fix #5971: admin menu is visible only if connected and user has ro...
Katja Luther

11/22/2016

05:32 PM Revision 48e61436 (cdmlib): fix sortindex updater and SynonymDeduplicator
Andreas Müller
10:18 AM bug #6206: Vaadin view fail with: Failed to load the bootstrap javascript
Please review Andreas Kohlbecker
10:03 AM bug #6206 (Resolved): Vaadin view fail with: Failed to load the bootstrap javascript
Applied in changeset commit:cdm-vaadin|a45e5ee72e1bc48fec16b156617c746266e1ccb4. Andreas Kohlbecker
09:32 AM bug #6206: Vaadin view fail with: Failed to load the bootstrap javascript
I examined the situation more in depth:
1. The pom.xml in cdm-webapp was pretty much messed up in respect of th...
Andreas Kohlbecker
09:19 AM bug #6206 (In Progress): Vaadin view fail with: Failed to load the bootstrap javascript
Andreas Kohlbecker
10:17 AM Revision 5dc7cec8 (cdm-webapp): ref #6206 cleaning up - removing commented section
Andreas Kohlbecker
10:03 AM Revision a45e5ee7 (cdm-vaadin): fix #6206 mapping one @WebServlets to the path /VAADIN/*
Andreas Kohlbecker
09:36 AM Revision 5c9f4ef1 (cdm-vaadin): minor - removing comment
Andreas Kohlbecker
09:22 AM Revision d0ded6af (cdm-webapp): ref #6206 solving problems with the war overlay and adding test d...
Andreas Kohlbecker

11/21/2016

05:27 PM bug #6211 (Closed): massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy
some requests to /portal/taxon/{uuid}/synonymy are causing a massive heap consumption.
test case:
* http://int...
Andreas Kohlbecker
04:55 PM Revision 7635cc7d (cdm-dataportal): ref #6201 fixing problem related to changes in taxon/{uuid}/a...
Andreas Kohlbecker
03:57 PM bug #6209 (Resolved): NPE in DatasourceView
Applied in changeset commit:taxeditor|af45abb87611c04e93d103bd7c7df6221ca9e877. Katja Luther
03:41 PM bug #6209: NPE in DatasourceView
This was a really confusing error message. The original problem was that the remote database was not available. Katja Luther
03:05 PM bug #6209 (Closed): NPE in DatasourceView
occurres when connection to remote datasource
~~~
java.lang.NullPointerException
at eu.etaxonomy.taxeditor.data...
Andreas Kohlbecker
03:56 PM Revision af45abb8 (taxeditor): fix #6209: adapt the message if a datasource is not available
Katja Luther
03:45 PM bug #6210 (Closed): Null values for boolean fields are causing PropertyAccessException
test case: http://int.e-taxonomy.eu/cdmserver/integration_cichorieae/portal/taxon/6d711fa0-77c3-42df-9d44-83fdc78f348... Andreas Kohlbecker
02:29 PM Revision 176a8641 (cdm-dataportal): removing unused variable
Andreas Kohlbecker
02:27 PM Revision 0c5a23b6 (cdm-dataportal): removing obsolte method argument
Andreas Kohlbecker
02:23 PM task #6208 (Rejected): implement synonymy service responding with DTO
The synonymy as returned by the is portal/taxon/{uuid}/synonymy is sometime quite huge and contains a lot of unused i... Andreas Kohlbecker
12:55 PM Revision 9128dcb4 (cdm-dataportal): ref #6201 adapting portal to changes in taxon/{uuid}/accepted...
Andreas Kohlbecker
11:51 AM Revision b19c294b (cdmlib): ref #5974 fixing LIE in controller
Andreas Kohlbecker
10:16 AM bug #6130 (Closed): Areafilter widget broken
works on the test server Andreas Kohlbecker
10:12 AM bug #6130 (Resolved): Areafilter widget broken
Applied in changeset commit:cdm-dataportal|ba127310d2b704049857de82c3c09e1bdc87092c. Andreas Kohlbecker
10:12 AM Revision ba127310 (cdm-dataportal): fix #6130 areafilter widget fixed
Andreas Kohlbecker

11/19/2016

01:55 PM feature request #5727 (Closed): Offer German translation for texts used in molecular plugin
Most translations have now been done. Translating will from now on be done directly in the development further of the... Ben Stöver
01:29 PM Revision 80e535dd (taxeditor): Additional strings externalized in molecular plugin.
Wizard for exporting single read alignments now warns and prompts if files are overwritten.
Bug fix: Changes in the f...
Ben Stöver
07:59 AM Revision 767e3890 (cdmlib-apps): ref #3934 fix factCategory SQL
Andreas Müller

11/18/2016

10:22 PM Revision ea2e509b (cdmlib): Cleanup
Andreas Müller
10:22 PM Revision f8dab136 (cdmlib): ref #3934 update Salvador import for facts
Andreas Müller
10:20 PM Revision b06dca5c (cdmlib-apps): ref #3934 update Salvador import for facts
Andreas Müller
08:05 PM Revision 060676fe (cdmlib): solving polytomouskey node sort index problems
Katja Luther
06:25 PM Revision e9773ade (taxeditor): ref #5971: new main menu admin with cdm preference nomenclatural c...
Katja Luther
05:01 PM Revision ecd0d355 (taxeditor): Messages edited.
Support for parameters to export only single reads or only consensus implemented.
JavaDoc extended.
Ben Stöver
04:45 PM Revision 521599f6 (cdmlib-apps): minor compile issues
Andreas Müller
04:40 PM Revision 3d037d99 (cdmlib): Latest BM import updates for Salvador
Andreas Müller
04:35 PM Revision 209a4cf6 (cdmlib-apps): ref #3934 Latest changes in Salvador import
Andreas Müller
04:35 PM Revision 805b65b2 (cdmlib-apps): Adapt BgbmInstancesUpdater to new databases
Andreas Müller
04:35 PM Revision 70f32474 (cdmlib-apps): Add nom. illeg. superfl. to allowed nom.states. without basionym...
Andreas Müller
04:35 PM Revision bf075ec4 (cdmlib-apps): Adapt BMTaxonRelationExport to new Synonym model
Andreas Müller
04:35 PM Revision 12c99f84 (cdmlib-apps): cleanup
Andreas Müller
04:26 PM Revision 8ec912fc (cdmlib-apps): Merge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-...
Andreas Müller
04:26 PM Revision 13ab8f7a (cdmlib-apps): minor
Andreas Müller
03:45 PM Revision a862b815 (taxeditor): Missing files from last commit added.
Ben Stöver
03:43 PM Revision 00d1a6ce (taxeditor): Export single read alignment wizard separated into two pages.
Option to elongate sequences added.
Application information parameters of JPhyloIO set.
Ben Stöver

11/17/2016

07:17 PM Revision 7417db95 (taxeditor): Exported single read sequences are now filled up with gaps. (Will ...
Texts in ExportSequenceToFileHandler extzernalized and translated. Ben Stöver
05:22 PM Revision d0c85dbc (taxeditor): Strings in ExportSingleReadAlignmentWizardPage externalized and tr...
Ben Stöver
02:11 PM bug #6207: Import Salvador images
Hallo,
zur Frage Image Server oder nicht: „Erstmal“ können wir das mit dem Standard Viewer machen, aber sobald wir m...
Andreas Müller
02:05 PM bug #6207 (New): Import Salvador images
Andreas Müller
01:40 PM Revision 02e8904c (taxeditor): Fixes in ExportSingleReadAlignmentWizardPage layout.
Default values added to ExportSingleReadAlignmentWizardModel.
Updating values after model binding in ExportSingleRead...
Ben Stöver
12:18 PM bug #6206 (Closed): Vaadin view fail with: Failed to load the bootstrap javascript
When testing any vaadin view the following error is shown
~~~
Failed to load the bootstrap javascript: ./../VAADI...
Patrick Plitzner
12:13 PM bug #6200 (Closed): Exception when adding a new synonym (allowOverride)
Update script has been adapted. Remove target version as this was a temporary issue only caused by model update comin... Andreas Müller
11:40 AM feature request #6198 (Resolved): Remove synonym relationships in TaxEditor
Andreas Müller
11:39 AM feature request #5971: Implement database wide CdmPreference writing
This is a subtask of the more general implementation described in #6105 (but more or less also a duplicate) Andreas Müller
10:09 AM Revision 6ecec98b (taxeditor): ref #6198 removed synonym type combobox
Patrick Plitzner
10:06 AM Revision c9d05940 (taxeditor): ref #6198 Correctly initialise ui field for pro parte and partial
Patrick Plitzner
10:05 AM Revision 4f57e9bf (taxeditor): ref #6205 Move excluded notes to the bottom of the wizard
Patrick Plitzner

11/16/2016

11:18 PM Revision 7ffbdbb1 (taxeditor): Export single read alignment wizard validation refactored and exte...
Some German translations in molecular plug-in added. Ben Stöver
09:25 PM Revision 661914be (taxeditor): Intermediate commit in implementing wizard validation (before movi...
Plug-in dependencies added to molecular. Ben Stöver
05:29 PM bug #6199 (Feedback): Excluded note for excluded taxon nodes in TaxEdtior
Looks like other additional languages are not stored correctly.
Also we may think about make it fully invisible as...
Andreas Müller
05:25 PM feature request #6197 (Closed): Move excluded and unplaced from Taxon to TaxonNode in TaxEditor
Works well. There is a follow up ticket #6205. Andreas Müller
05:24 PM bug #6205 (Duplicate): Move excluded nodes to the bottom of the list in TaxEditor navigator
... and also ad a symbol to the node that shows that it is excluded.
We may also think about adding a "set to excl...
Andreas Müller
05:17 PM feature request #6198 (Feedback): Remove synonym relationships in TaxEditor
Andreas Müller
05:16 PM feature request #6198: Remove synonym relationships in TaxEditor
There is a more general issue related to #5523 and #5877.
Currently the synonym type is not handled correctly by t...
Andreas Müller
05:13 PM feature request #6198: Remove synonym relationships in TaxEditor
It looks like partial and pro parte is not persisted. Andreas Müller
04:52 PM feature request #5778 (Closed): Update symbols for PresenceAbsenceTerms in existing databases
Andreas Müller
04:32 PM bug #5826 (Closed): Clean up names with empty name descriptions
Andreas Müller
04:23 PM feature request #5921 (Closed): Change symbol for congruence relationship.
Andreas Müller
04:21 PM feature request #5981 (Closed): Add abbreviation to Rank "Cultivar"
Andreas Müller
10:57 AM bug #4965: unsupported method getDatabase() in WrappedCdmDataSource breaks forceSchemaUpdate
Please review the latest change 32e833cb Andreas Müller
10:47 AM feature request #5634 (Closed): Excluded note for excluded taxa /taxon nodes
Andreas Müller
10:46 AM feature request #6204 (New): Show excludedNote in dataportal
for more information see model change ticket #5634. The new field should be shown in the dataportal (maybe configurab... Andreas Müller
10:43 AM feature request #5875 (Closed): Add isDefault flag to DescriptionBase
Andreas Müller
10:40 AM feature request #5952 (Closed): Second cache field for specimen (identityCache)
Andreas Müller
10:38 AM bug #5976 (Closed): Update sortIndex for potential nullValue sortIndexes
Andreas Müller
10:37 AM task #6089 (Closed): Remove taxonomicParentCache and taxonomicChildrenCount from Taxon
Andreas Müller

11/15/2016

05:33 PM Revision 8fb27488 (cdmlib): ref #4867 Set sec reference for taxa in cloned classification
Patrick Plitzner
05:28 PM bug #6199 (Resolved): Excluded note for excluded taxon nodes in TaxEdtior
Applied in changeset commit:taxeditor|ac1659d4fb4bd6a0f42c5e3cef97dee1ccad7925. Patrick Plitzner
05:27 PM Revision ac1659d4 (taxeditor): fix #6199 Excluded note for excluded taxon nodes in TaxEditor
Patrick Plitzner
05:27 PM bug #6200: Exception when adding a new synonym (allowOverride)
In my case setting the only one existing preference for which code to use to 0 solved the problem. Before the value w... Patrick Plitzner
12:29 PM bug #6200: Exception when adding a new synonym (allowOverride)
This was probably an issue in the update script. Fixed now, but for database which already ran the update script you ... Andreas Müller
12:24 PM bug #6200 (Resolved): Exception when adding a new synonym (allowOverride)
Applied in changeset commit:cdmlib|b6ee6df472c8eaccb21369ebd429e9feacc78e36. Andreas Müller
10:58 AM bug #6200 (Closed): Exception when adding a new synonym (allowOverride)
1. In any DB press enter in the name editor to create a new synonym
1. The following error is logged
~~~
org.h...
Patrick Plitzner
05:09 PM Revision 924ba372 (taxeditor): ExportSingleReadAlignmentWizard now exposes whole format info object.
FileDialog added to ExportSingleReadAlignmentWizardPage. Ben Stöver
03:11 PM Revision 94e60697 (taxeditor): Clean up Derivate perspective
- Remove Derivate view as it is not a view but an editor (they have
their own designated area)
Patrick Plitzner
03:10 PM Revision 48005c5f (taxeditor): Fix potential NPE
Patrick Plitzner
03:03 PM feature request #3925 (Closed): Unplaced and excluded to TaxonNode
Andreas Müller
03:00 PM feature request #6203 (New): Implement unplaced and excluded in dataportal
~~The unplaced and excluded flags have been moved from Taxon to TaxonNode (#3925). This should be taken in account in... Andreas Müller
02:54 PM bug #3658 (Closed): Update Nomenclatural code for datasources
Andreas Müller
02:53 PM bug #6202 (New): Disable "New" button in toolbar when editor is not connected
The options are not filtered like those in the menu bar and can produce exceptions Patrick Plitzner
02:50 PM bug #6201 (Closed): Adapt dataportal to the new synonym datamodel
Synonym relationships have been removed. Synonyms do now directly link to accepted taxa. This needs to be adapted in ... Andreas Müller
02:41 PM feature request #5971: Implement database wide CdmPreference writing
allowOverride #5970 is now fixed, so we can finalize this task. Andreas Müller
02:22 PM feature request #5970 (Closed): Implement allowOverride in CdmPreference
Andreas Müller
02:21 PM feature request #5970: Implement allowOverride in CdmPreference
This is fully resolved now. Please update taxeditor accordingly if needed. Andreas Müller
12:42 PM bug #5976 (Resolved): Update sortIndex for potential nullValue sortIndexes
PKNode also implemented now. Should be resolved. Andreas Müller
12:23 PM Revision b6ee6df4 (cdmlib): fix #6200 Change order of NomenclaturalCodeUpdater and allowOverride ...
Andreas Müller
11:37 AM Revision b1b8716e (cdmlib): Remove deprecated adder methods for multilanguage text
Andreas Müller
11:34 AM Revision 85b59453 (cdmlib): ref #5634 add getter and putter for excluded note
Andreas Müller
11:07 AM Revision b7c0b206 (cdmlib): cleanup and javadoc
Andreas Müller
11:07 AM Revision 93ad47c4 (cdmlib): ref #5976 add PKNode sortindex update
Andreas Müller
10:51 AM feature request #6198 (Resolved): Remove synonym relationships in TaxEditor
Applied in changeset commit:taxeditor|69410b96c9c8e1e23d68cd782867171c2e1cd084. Patrick Plitzner
10:50 AM feature request #6197 (Resolved): Move excluded and unplaced from Taxon to TaxonNode in TaxEditor
Applied in changeset commit:taxeditor|3e194787899d08624921b3b5cbb109ebcc74b4f5. Patrick Plitzner
10:50 AM Revision 69410b96 (taxeditor): fix #6198 Remove synonymrelationships in TaxEditor
Patrick Plitzner
10:12 AM Revision 3e194787 (taxeditor): fix #6197 Move excluded and unplaced from Taxon to TaxonNode in
TaxEditor Patrick Plitzner
09:47 AM Revision fdefb4bc (taxeditor): Fix possible widget is disposed exception
Patrick Plitzner
09:35 AM Revision e701bdea (taxeditor): Fix potential NPE
Patrick Plitzner
08:45 AM Revision 45844ac2 (cdmlib): ref #5974 fix update script for synonym duplicates
Andreas Müller
08:43 AM Revision eaf29c2e (cdmlib): cleanup
Andreas Müller

11/14/2016

07:34 PM Revision bcb823d5 (taxeditor): Missing dependency Apache commons.lang added to molecular.lib.
Single read alignment export feature now makes use of wizard. (Selecting which sequences to export is not yet support... Ben Stöver
05:34 PM Revision 9a9359ce (taxeditor): New JPhyloIO package now exported by molecular.lib.
SingleReadAlignmentPredicates renamed to SingleReadAlignmentRDFXMLConstants.
Pherogram alignment shifts are now writt...
Ben Stöver
04:12 PM Revision fc53d911 (taxeditor): cleanup
Andreas Müller
04:12 PM Revision 0d726c87 (taxeditor): Move MoveTaxonOperationTest to navigation package and try to enable
Andreas Müller
03:58 PM bug #6199: Excluded note for excluded taxon nodes in TaxEdtior
Please ask Katja if unclear how to implement. Andreas Müller
03:56 PM bug #6199 (Closed): Excluded note for excluded taxon nodes in TaxEdtior
See related ticket #5634 for more information.
We need to add a multi-language field here.
Andreas Müller
03:52 PM feature request #6198 (Closed): Remove synonym relationships in TaxEditor
See parent ticket for more information.
The according elements have been commented in existing DetailsSection(s). ...
Andreas Müller
03:48 PM feature request #6197 (Closed): Move excluded and unplaced from Taxon to TaxonNode in TaxEditor
See parent ticket for more information.
The according field have been commented in existing DetailsSection(s). Ple...
Andreas Müller
02:38 PM Revision e042ef3a (taxeditor): ref #5875 fix testdata in TaxEditor
Andreas Müller
02:27 PM Revision b3570263 (taxeditor): ref #5875 fix testdata in TaxEditor
Andreas Müller
02:26 PM Revision d837c623 (taxeditor): add gitignore
Andreas Müller
02:13 PM Revision d0899d41 (taxeditor): ref #3925 fix testdata in TaxEditor
Andreas Müller
02:01 PM Revision 18336f56 (taxeditor): ref #3925 fix testdata in TaxEditor
Andreas Müller
01:39 PM Revision 9300078c (taxeditor): ref #3925 fix testdata in TaxEditor
Andreas Müller
01:38 PM Revision 7f30d120 (taxeditor): Clean up
Andreas Müller
01:20 PM Revision 71cfddb2 (taxeditor): ref #3925 fix testdata in TaxEditor
Andreas Müller
01:19 PM Revision 4fe73167 (taxeditor): clean up
Andreas Müller
01:19 PM Revision 478830af (taxeditor): Add dataset.dtd to TaxEditor test data
Andreas Müller
01:05 PM bug #6195 (New): suppress footnotes in search results page
showing annotations in the results page is not only undesirable but also slows down the page rendering process. Andreas Kohlbecker
10:57 AM Revision a0069258 (taxeditor): Try to reinstall tests for MoveTaxonOperation (maybe not yet correct)
Andreas Müller
10:56 AM Revision 691ace9e (taxeditor): Cleanup
Andreas Müller
10:56 AM Revision c81df78d (taxeditor): Update testdata in TaxEditor to model changes
Andreas Müller
10:19 AM Revision e4e86d74 (taxeditor): Update TaxEditor tests to model changes
Andreas Müller
09:44 AM bug #6131 (Closed): Vaadin DistributionEditor TODOS
Patrick Plitzner
09:26 AM Revision 9fe639a8 (cdm-vaadin): ref #6131 Redirect for old URLs
- deleted test ui class Patrick Plitzner

11/13/2016

06:24 PM Revision 0608d733 (taxeditor): ExportSingleReadAlignmentWizardPage now allows to select output fi...
format. Ben Stöver

11/11/2016

02:18 PM Revision e73a46a0 (taxeditor): ref #5974 Some synonymRelationship updates in TaxEditor tests
Andreas Müller
02:07 PM Revision 1b945f03 (taxeditor): ref #5974 Some synonymRelationship updates
Andreas Müller
01:58 PM Revision aa01111e (taxeditor): ref #5974 Some synonymRelationship updates and update for dataset....
Andreas Müller
01:52 PM bug #6194 (Duplicate): can't enter a new reference from feature data (Faktendaten)
1. created description of a new fact for a taxon (Corvidae)
2. wanted to add a reference
3. reference was not yet i...
Gabriele Dröge
01:43 PM Revision 96387738 (taxeditor): Revert "update model for cdm cache in TaxEditor" classpath changes
This partly reverts commit cfb2c8db2bd6905fd8b5805915556b87af14984f. Andreas Müller
01:41 PM Revision cfb2c8db (taxeditor): update model for cdm cache in TaxEditor
Andreas Müller
01:14 PM Revision 10035678 (taxeditor): update TaxEditor H2 test database to new model
Andreas Müller
01:12 PM Revision ceb3e3f3 (cdmlib): ref #3925 and #5974 Improve update script for non unique subqueries
Andreas Müller
12:35 PM bug #6192 (New): taxon annotations only shown when 'Show accepted taxon on top of the synonymy' ...
taxon annotations are missing when 'Show accepted taxon on top of the synonymy' is not enabled in http://portal.cyb... Andreas Kohlbecker
12:12 PM bug #6157: Consider implementing quick setup button "Quick Singlepage Configuration'"
Walter: Diese Beschreibung habe ich in die Doku aufgenommen - wenn das anders implementiert wird, bitte bescheid sagen. Walter Berendsohn
11:23 AM Revision c67d01cb (cdmlib): ref #5970 remove transient from allowOverride
Andreas Müller
10:55 AM Revision dc54e76e (taxeditor): ref #3925 remove unplaced and excluded from taxon view
Andreas Müller

11/10/2016

04:30 PM Revision e7c1e4aa (cdmlib): Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into...
Andreas Müller
02:49 PM Revision 9c48245f (cdmlib): delete TestCase from BioCaseQueryServiceWrapper
Katja Luther
01:50 PM Revision 0d2ee5d6 (taxeditor): fix #4461 fix ordering for Datasource View
Andreas Müller
01:50 PM Revision 266b34fd (taxeditor): cleanup
Andreas Müller
01:50 PM Revision 9e4b94cb (taxeditor): ref #3658 remove nomenclatural code from datasources
Andreas Müller
01:50 PM Revision df95e395 (taxeditor): cleanup
Andreas Müller
01:50 PM Revision 10644642 (taxeditor): ref #3658 remove nomenclatural code from datasources
Andreas Müller
01:50 PM Revision bdd1bcf5 (taxeditor): ref #5974 Remove synonym relationships (rename synRelType to synRe...
Andreas Müller
01:50 PM Revision 5215f59f (taxeditor): ref #3658 remove nomenclatural code from datasources
Andreas Müller
01:50 PM Revision d34abf30 (taxeditor): ref #5974 Remove synonym relationships (compiling)
Andreas Müller
01:45 PM Revision 5521f23c (cdm-vaadin): Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdm-vaa...
Andreas Müller
01:32 PM Revision 92afad3d (cdmlib-apps): Merge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-...
Conflicts:
app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
app-import/src/main/java/eu/et...
Andreas Müller
01:09 PM Revision f3fc1024 (cdmlib): Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into...
Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TaxonInteraction.java
cdmlib-services/src/...
Andreas Müller
12:54 PM Revision b6e8ecc0 (cdmlib-apps): Cleanup and remove deprecated method
Andreas Müller
12:53 PM Revision 1ba3392b (cdmlib-apps): Update Salvador import
Andreas Müller
12:48 PM Revision e25fecb9 (cdmlib): cleanup
Andreas Müller

11/09/2016

04:08 PM Revision 49bb0781 (taxeditor): i18n for AuthenticationUserBar
Patrick Plitzner
02:57 PM bug #6191: Update context menu in name editor after "Change to accepted taxon"
This behavior was observed during the Rote Liste 2020 Workshop in Nov. 2016 Andreas Müller
12:37 PM bug #6191 (New): Update context menu in name editor after "Change to accepted taxon"
menu options are not refreshed after operation is done Patrick Plitzner
11:33 AM bug #6190 (Closed): remove svn property place holder in first line of code
The first line of almost each java code file is a special place holder '// $Id$' which was meant to be replaced by th... Andreas Kohlbecker

11/08/2016

04:41 PM bug #6115: protect cdm content by drupal permission
I fixed the above described bug. Please test again.
NOTE: There is a new section in the description on how to test...
Andreas Kohlbecker
04:38 PM bug #6115 (Resolved): protect cdm content by drupal permission
Applied in changeset commit:cdm-dataportal|239c4040ea26be2c36b2344e4aa276f27bee55db. Andreas Kohlbecker
01:34 PM bug #6115: protect cdm content by drupal permission
Andreas Müller wrote:
> Currently the taxon tree is still shown at Flora Malesiana: http://test.e-taxonomy.eu/datapo...
Andreas Kohlbecker
01:15 PM bug #6115: protect cdm content by drupal permission
Currently the taxon tree is still shown at Flora Malesiana: http://test.e-taxonomy.eu/dataportal/preview/flora-malesi... Andreas Müller
12:27 PM bug #6115 (In Progress): protect cdm content by drupal permission
The protection can be by passed by accesing the the content via the drupal node integration. An according check must ... Andreas Kohlbecker
04:37 PM Revision 239c4040 (cdm-dataportal): fix #6115 adding missing permission check to cdm nodes integr...
Andreas Kohlbecker
04:22 PM bug #6186 (Rejected): Drupal nodes are created even if Create drupal nodes is off
cannot reproduce this
I tested this with the following portals in which all CDM nodes have been deleted now:
*...
Andreas Kohlbecker
12:29 PM bug #6186 (Worksforme): Drupal nodes are created even if Create drupal nodes is off
This refers to the setting admin/config/cdm_dataportal/settings#edit-cdm-drupal-node-creation Andreas Kohlbecker
03:07 PM feature request #6041 (In Progress): Change the label of "Set as basionym of homotypical group"
Andreas Müller
02:47 PM feature request #6041: Change the label of "Set as basionym of homotypical group"
Set back to unassigned CDM tickets as first child tickets have to be resolved. Andreas Müller
02:40 PM feature request #6188 (New): Make "Set as basionym of homotypical group" an optional function
See parent ticket. Still needs discussion if this is really wanted. Andreas Müller
02:36 PM feature request #6187 (New): [DISCUSS] Ask W.Greuter about "type providing name"
See parent ticket Andreas Müller
02:32 PM bug #6174 (Closed): LIE when deleting new name
Seems to be fixed Andreas Müller
02:29 PM Revision b22621fd (cdm-vaadin): ref #5458 Avoid possible exception for case sensitive root node c...
Patrick Plitzner
02:23 PM Revision ae5a0d99 (cdmlib): Minor changes to classification clone method
Andreas Müller
02:22 PM Revision 104cc879 (cdmlib): Clean up
Andreas Müller
02:21 PM Revision a6f3a18c (cdmlib): Clean up deprecated methods in name service
Andreas Müller
02:00 PM Revision 9bb42d8a (cdm-vaadin): ref #5458 Fix node retrieval for classification
Patrick Plitzner
01:53 PM Revision bea4aa93 (cdm-vaadin): ref #5458 label for null selection (remove status)
Patrick Plitzner
01:48 PM Revision 8a6e2f9a (cdm-vaadin): ref #5458 Refresh titlecache of named area vocabularies
Patrick Plitzner
01:47 PM Revision f9ea11c9 (cdm-vaadin): ref #5458 Allow one-click selection for status term
Patrick Plitzner
01:45 PM bug #6023 (Closed): configuration problems with maven-antrun-plugin
Seems to work. I also tested the latest build on a machine with java 1.7 installed (pesihpc) and got no problems. Andreas Müller
01:40 PM Revision 82a22019 (cdmlib): Cleanup
Andreas Müller
01:38 PM bug #6176 (Closed): Creating a new Reference throws TOE (TransientObjectException)
Seems to be fixed. I remove target version as it was a temporary regression only. Andreas Müller
01:36 PM feature request #5972: Prevent user from unwanted author and reference updates
It looks like it wokrs only for references until now. But we need it for all objects (if this is difficult, at least ... Andreas Müller
01:34 PM feature request #5972 (Feedback): Prevent user from unwanted author and reference updates
I would change the label to "This reference is referenced by xxx records. The change will take for all these records.... Andreas Müller
12:11 PM bug #5692 (Closed): Delete a person within the bulk editor deletes the person even if not saved
Seems to be fully fixed now. Great. Andreas Müller
12:04 PM bug #5680 (Closed): Out-of-Memory when editing TaxonInteraction
Seems to be fixed. There might be some other such issues. See #3841 Andreas Müller
09:34 AM bug #5680 (Resolved): Out-of-Memory when editing TaxonInteraction
Applied in changeset commit:cdmlib|4b5eb627a4a79b7dfb7588779e1ef566a69c8ecc. Katja Luther
09:33 AM bug #5680: Out-of-Memory when editing TaxonInteraction
The problem was the naming of the getter method for description. It was getDescriptions() but should be getDescriptio... Katja Luther
10:26 AM Revision c9181133 (cdmlib): ref #4866 Set sec reference for taxa when cloning classification
Patrick Plitzner
10:21 AM task #6158: Update EDIT documentation from svn to git
Also generally try to update the site where necessary. E.g. java version is now 1.7 Andreas Müller
10:04 AM Revision 211add74 (taxeditor): smaller changes to display taxon interactions
Katja Luther
10:04 AM Revision 935960dc (taxeditor): ref #6176: the referencingObjectsCount is only called for wizards ...
Katja Luther
09:48 AM Revision a663859a (cdmlib): minor
Katja Luther
09:46 AM Revision aede647b (cdmlib-apps): adapt getDescription() see #5680
Katja Luther
09:42 AM Revision 4b321494 (cdm-vaadin): ref #5458 Fix node retrieval and taxonTree refresh
Patrick Plitzner
09:36 AM bug #6077 (Closed): Import of gathering images
Katja Luther
09:32 AM Revision 205b4b75 (cdmlib): missed to add the adapted test
Katja Luther
09:28 AM Revision 4b5eb627 (cdmlib): fix #5680: get method needs to be named like the attribute
Katja Luther
09:16 AM Revision ba0e4a8c (cdm-vaadin): ref #5458 Allow null selection to remove distribution status
Patrick Plitzner

11/07/2016

01:04 PM Revision 6dd0db6f (cdmlib): switching maven-jetty plugin back to jdk 1.7 compatible version
Andreas Kohlbecker
12:35 PM Revision ef6db0d3 (cdm-vaadin): lowering java target version to 1.7
Andreas Kohlbecker
12:17 PM bug #6023 (Resolved): configuration problems with maven-antrun-plugin
Applied in changeset commit:cdmlib|1ddde622ae10b01976cdb99fb50a469a5506ca7e. Andreas Kohlbecker
12:17 PM bug #6023 (In Progress): configuration problems with maven-antrun-plugin
Andreas Kohlbecker
12:16 PM Revision 1ddde622 (cdmlib): fix #6023 solving compatibility problems of aspectj with java 1.8 and...
Andreas Kohlbecker
11:45 AM Revision c7bddd78 (cdm-vaadin): gitignore
Andreas Kohlbecker
11:45 AM Revision 0cb4f241 (cdm-vaadin): setting vaadin production mode to true - globally
Andreas Kohlbecker
11:45 AM Revision 201dfb32 (cdm-vaadin): ref #5862 adding missing dependency to provide missing xsd when o...
Andreas Kohlbecker
11:45 AM Revision d436d94e (cdm-vaadin): adding developer logging config to ide launcher
Andreas Kohlbecker
11:45 AM Revision abbbb46c (cdm-vaadin): disabling SuperDev mode which is now on by default
Andreas Kohlbecker
11:45 AM Revision cd760b09 (cdm-vaadin): fixing double servlet mapping
Andreas Kohlbecker
11:45 AM Revision 479b0055 (cdm-vaadin): simplifying dependencies in pom.xml (using scope 'compile' where ...
Andreas Kohlbecker
11:45 AM Revision ca950879 (cdm-vaadin): removing scope provided from launcher
Andreas Kohlbecker
11:45 AM Revision 974ae00d (cdm-vaadin): updating DataSourceConfigurer with new code from cdmlib-remote - ...
Andreas Kohlbecker
11:45 AM Revision 25c1d6d8 (cdm-vaadin): fixin project setup:
- solving maven warnings
- solving some dependency problems (itextpdf, ...)
- solving dependency probelms with je...
Andreas Kohlbecker
11:45 AM Revision 2693d2d2 (cdm-vaadin): fixing startup, dependency problems of jetty
- fixed for eclipse ide
- fixed for maven-jetty plugin
Andreas Kohlbecker
11:45 AM Revision ab7b3cd1 (cdm-vaadin): fixing dependency management problems
- letting versions be managed through cdmlib-parent
- depending project on cdmlib-remote
- removing classes clone...
Andreas Kohlbecker
11:28 AM Revision 5a9620a0 (cdmlib): updating maven-jetty plugin
Andreas Kohlbecker
10:43 AM bug #5862: Spring needs online resources during launch
a much better solution is to let the versions be managed through the pom.xml of cdmlib-parent:
~~~xml
<dependen...
Andreas Kohlbecker
10:41 AM bug #5862 (Resolved): Spring needs online resources during launch
Applied in changeset commit:cdmlib-apps|a6c3d024c6c3121786f55c474655f4f1dd2fd2a2. Andreas Kohlbecker
10:41 AM Revision a6c3d024 (cdmlib-apps): fix #5862 by correctly managing dependencies
Andreas Kohlbecker
10:31 AM Revision dd998643 (cdmlib-apps): managing cdmlib dependencies
Andreas Kohlbecker
09:52 AM Revision 96661f94 (cdmlib): smaller changes for abcd import
Katja Luther
09:51 AM Revision 2704bbc5 (cdmlib): revert adding error log
Katja Luther
09:43 AM Revision 3522e0b1 (cdmlib): minor
Katja Luther
09:42 AM Revision 57089e91 (cdmlib): minor
Katja Luther
09:33 AM Revision ce790c77 (cdmlib): ref #6166: import siblings if an specimen and smaller changes in ABCD
import Katja Luther

11/06/2016

02:22 PM Revision 66e8ec64 (cdmlib): ref #4866 Fix transient object exception
- fixed typo Patrick Plitzner
02:21 PM Revision 5d3fd02f (taxeditor): ref #4867 Implement "Clone Classification" functionality
- availabel via context menu in taxon navigator
- parameters available: classification name, taxon relation from clo...
Patrick Plitzner
01:00 PM Revision 7e313273 (cdmlib): ref #4866 Create new description set when cloning taxon (avoid
HibernateException) Patrick Plitzner
01:00 PM Revision 355c89cb (cdmlib): ref #4866 First implementation for clone classification (including test)
Patrick Plitzner
01:00 PM Revision cea52158 (cdmlib): ref #5449 Imporvements for CSV export
- Fix initialization problems
- Correctly match taxon name to chosen classification
- allow export for single leaf ...
Patrick Plitzner
01:00 PM Revision 7d8eced5 (cdmlib): ref #4866 Test for first implementation for clone classification
Patrick Plitzner

11/04/2016

11:20 PM Revision 1925e9f2 (cdm-vaadin): ref #5974 Fix synonymRelationship issues in vaadin
Andreas Müller
05:01 PM Revision 35b0416a (cdmlib): adapt gestGetUuidAndTitleCache data to new model
Andreas Müller
04:19 PM Revision f35df403 (cdmlib-apps): change the versions to 4.4
Katja Luther
04:12 PM Revision 4bcc0c85 (cdmlib): fix compile error in ITaxonNodeService
Andreas Müller
03:04 PM Revision b811f6b1 (cdm-vaadin): cleanup
Andreas Müller
02:48 PM Revision 3df95930 (cdm-vaadin): Update test H2 in vaadin to new model
Andreas Müller
02:47 PM Revision 47936c60 (cdm-vaadin): ref #5974 remove synonym relationship and other model changes
Andreas Müller
02:36 PM Revision e82b27f2 (cdm-vaadin): cleanup
Andreas Müller
02:09 PM Revision 0e522f9f (cdm-vaadin): ref #5974 Remove synonym relationships
Andreas Müller
02:08 PM Revision 4b6abd7e (cdmlib): Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/cdmlib into...
Conflicts:
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ITaxonNodeService.java
Andreas Müller
12:42 PM bug #5862 (In Progress): Spring needs online resources during launch
This can be solved by adding the spring dependency which provides the missing xsd file in the jar.
I fixed this fo...
Andreas Kohlbecker
09:25 AM bug #5692 (Resolved): Delete a person within the bulk editor deletes the person even if not saved
The transient objects can be deleted now without exception see #6175 Katja Luther
09:23 AM bug #6159: improve distribution editor in TaxEditor
@AM and @Patrick
please have a look if this is ok for next week.
Katja Luther
09:19 AM bug #6176 (Resolved): Creating a new Reference throws TOE (TransientObjectException)
Katja Luther
09:19 AM bug #6176: Creating a new Reference throws TOE (TransientObjectException)
Andreas Müller wrote:
> Sorry, I think I have to reopen this ticket for a general question.
>
> I do not understa...
Katja Luther

11/03/2016

04:58 PM bug #6175 (Closed): Exception when deleting transient object
Seems to work now. Remove target version as this issue was only a temporary regression. Fixed in v4.4 snapshot Andreas Müller
02:19 PM bug #6175: Exception when deleting transient object
Applied in changeset commit:taxeditor|734218f995535b1920b9feb5eab9e91141e0c536. Katja Luther
02:18 PM bug #6175 (Resolved): Exception when deleting transient object
This was related to the last change in the bulk editor that the objects which should be deleted are marked as deleted... Katja Luther
09:34 AM bug #6175: Exception when deleting transient object
I think that this is not related to the getReletatedObjectsCount problem. This was easily fixed by checking if the en... Katja Luther
04:47 PM bug #5870 (Closed): NPE when trying to open a synonym (or taxon) that has been deleted
Andreas Müller
04:42 PM bug #6122 (Feedback): add titleCache service
There still seems to be an issue as the result for cuba classification on test is empty: http://test.e-taxonomy.eu:80... Andreas Müller
04:35 PM bug #6122: add titleCache service
Please review Andreas Müller
04:39 PM bug #6180 (Rejected): NoSuchMethodException: getUuidAndTitleCacheTaxon on attempt to add taxon to...
In deed I was using an incompatible editor Andreas Kohlbecker
01:02 PM bug #6180 (Resolved): NoSuchMethodException: getUuidAndTitleCacheTaxon on attempt to add taxon to...
This is probably a version issue as otherwise a compilation error should occur. Please check. Andreas Müller
12:22 PM bug #6180 (Rejected): NoSuchMethodException: getUuidAndTitleCacheTaxon on attempt to add taxon to...
To reprododuce:
* data source http://test.e-taxonomy.eu/cdmserver/phycobase/
1. Create new description for any ...
Andreas Kohlbecker
04:30 PM bug #6129 (Closed): After creating a new Reference in selection dialog, it could not be found in ...
Andreas Müller
03:57 PM bug #6129: After creating a new Reference in selection dialog, it could not be found in the selec...
Seems to work now. Andreas Müller
04:18 PM bug #6176 (Feedback): Creating a new Reference throws TOE (TransientObjectException)
Sorry, I think I have to reopen this ticket for a general question.
I do not understand why the "getReferencingObj...
Andreas Müller
04:09 PM bug #6176 (Closed): Creating a new Reference throws TOE (TransientObjectException)
Seems to be fixed. As it was only a temporary regression within v4.4 snapshot caused by #5972 I remove the target ver... Andreas Müller
09:39 AM bug #6176: Creating a new Reference throws TOE (TransientObjectException)
added a check for the id to confirm whether the entitiy is new or not. This fixed the problem. Katja Luther
09:38 AM bug #6176 (Resolved): Creating a new Reference throws TOE (TransientObjectException)
Applied in changeset commit:taxeditor|384b41bd24d4ca11f044bb6cce1f8fc5845e621c. Katja Luther
04:05 PM bug #6178 (Duplicate): TOE Exception when creating a new Reference
Looks like this was fixed together with #6178. As it was only a temporary regression within v4.4 snapshot I remove th... Andreas Müller
03:46 PM feature request #5972 (Resolved): Prevent user from unwanted author and reference updates
Andreas Müller
03:44 PM bug #6181: Deleting a misapplied name does not set the dirty flag
So this is an other issue for our save strategy ticket (please link). Because this is unclear for the user who expect... Andreas Müller
03:03 PM bug #6181: Deleting a misapplied name does not set the dirty flag
That is correct because it is already persisted to the DB. This is because the deletion of the misapplied name is a s... Katja Luther
02:57 PM bug #6181 (New): Deleting a misapplied name does not set the dirty flag
This happens in NameEditor.
Found in v4.4 snapshot.
Andreas Müller
03:32 PM bug #5948 (Closed): supress protologue icon if according media uri is missing
Seems to be fixed. I only found a related Editor issue #6182. Andreas Müller
03:30 PM bug #6182 (New): Emptying protolog URI does not work
The protolog URI field can not be fully emptied but only deleted.
If you empty the protolog field and save this no...
Andreas Müller
02:48 PM bug #5676 (Feedback): Sensu does not show up if no author exists for secundum reference
This seems to work fine now.
The only open question is "Also I wonder if it is wanted behavior, that the publicati...
Andreas Müller
02:41 PM Revision 08a29cf3 (taxeditor): the pattern for new created nomenclatural references with nomencla...
Katja Luther
02:19 PM bug #6174 (Resolved): LIE when deleting new name
Applied in changeset commit:cdmlib|645658b9cc716e53f2a6ccf1d8d200c771c1a4c6. Katja Luther
02:09 PM bug #6174: LIE when deleting new name
this is fixed by changing the args of isDeletable to UUID. Katja Luther
09:30 AM bug #6174: LIE when deleting new name
the original exception is :
~~~ text
org.hibernate.LazyInitializationException: failed to lazily initialize a col...
Katja Luther
02:19 PM Revision 734218f9 (taxeditor): fix #6175: transient objects are not marked as deleted in bulk edi...
Katja Luther
02:04 PM Revision 645658b9 (cdmlib): fix #6174: isDeletable needs to be called with UUID and the objects is
loaded on server side Katja Luther
10:12 AM Revision 87f819cf (cdmlib): ref #5458 Add classification filter to service method
Patrick Plitzner
10:12 AM Revision e8a3d3c8 (cdm-vaadin): ref #5458 Fix potential SQL query syntax exception
Patrick Plitzner
09:52 AM Revision a4f62469 (taxeditor): add a new DeleteMediaConfiguratorComposite
Katja Luther
09:49 AM Revision 6fe75af3 (cdmlib): fix media deletion
Katja Luther
09:43 AM bug #6179 (New): Use @RestController where appropriate

a good summary : https://dzone.com/articles/spring-framework-restcontroller-vs-controller?edition=237194&utm_source...
Andreas Kohlbecker
09:41 AM bug #5692: Delete a person within the bulk editor deletes the person even if not saved
The media bulk editor is fixed now see Revision f1a1a089. The problem of deleting a transient object still exists. Katja Luther
09:40 AM Revision f1a1a089 (taxeditor): fix the deletion of media in bulk editor
Katja Luther
09:37 AM Revision 384b41bd (taxeditor): fix #6176: check if entity is new
Katja Luther

11/02/2016

11:52 PM bug #6176: Creating a new Reference throws TOE (TransientObjectException)
This is very similar to #6178 (but not exactly a duplicate I guess) Andreas Müller
05:14 PM bug #6176 (Closed): Creating a new Reference throws TOE (TransientObjectException)
What I did:
* Open reference bulk editor
* Create a new Reference via "new", e.g. "Test Reference" (Generic)
* W...
Andreas Müller
11:51 PM bug #6178: TOE Exception when creating a new Reference
This issue is very similar to #6176 (but not exactly a duplicate I guess) Andreas Müller
11:48 PM bug #6178 (Duplicate): TOE Exception when creating a new Reference
I tried to add a new nomencl. reference via "Create a new Reference in Reference selection dialog.
This caused the f...
Andreas Müller
08:28 PM feature request #6058 (Feedback): Store NamedArea dialog filters more individually
All Area lists like (geoscope in classification or PolytomousKey) seem to handle "Add" and "Edit" differently which d... Andreas Müller
07:34 PM feature request #5891 (Closed): Taxon appended phrase should not allow empty string
Fixed Andreas Müller
07:09 PM bug #5888 (Closed): Deleting factual data does not work (dirty flag not set)
Seems to work Andreas Müller
06:31 PM bug #5800 (Closed): Remove "Taxonomically Included In" from list of concept relationship types
Seems to work. There is a related issue #6177. Andreas Müller
06:30 PM bug #6177 (New): Taxon Concept relationship type not editable in details view
For some reason the Relationship Type field in the Taxon Concept relationship details view is not editable.
I can't ...
Andreas Müller
06:01 PM bug #5692: Delete a person within the bulk editor deletes the person even if not saved
While testing I found 3 other issues that might be related. #6174, #6175, #6176. Please check if they are regressions... Andreas Müller
06:00 PM bug #5692 (Feedback): Delete a person within the bulk editor deletes the person even if not saved
Looks like Media bulk editor is not yet fixed! All others seem to work. Andreas Müller
04:01 PM Revision ad0d2649 (cdm-vaadin): ref #5458 Notify user when taxon tree is loading
Patrick Plitzner
03:15 PM bug #6175 (Closed): Exception when deleting transient object
What I did
* Open bulk editor (name or agent)
* Run a search (with >0 results)
* Create a new record
* Immediat...
Andreas Müller
03:05 PM bug #6174: LIE when deleting new name
It looks like the error does not happen always. So please play around a bit, also with different order for save, sear... Andreas Müller
02:54 PM bug #6174 (Closed): LIE when deleting new name
What I did:
* Open name bulk editor
* Create new name (e.g. Testus species)
* Save
* Search for Testus*
* Dele...
Andreas Müller
02:01 PM bug #6165 (Rejected): distributionInfoFor service no longer respects the statsusColors parameter
This issue is a data issue related to merges of presence absence terms (#5778). The hardcoded colors have been change... Andreas Müller
12:40 PM Revision 246e313b (cdm-vaadin): ref #5458 Clear caches when re-initializing table view
Patrick Plitzner
12:04 PM Revision f5b90187 (cdm-vaadin): ref #5458 Performance and usability
- avoid re-initialization of distribution settings
- removed Save button
Patrick Plitzner
09:19 AM Revision 787028b1 (cdm-vaadin): ref #5458 Fix some intitialization problems
Patrick Plitzner

11/01/2016

04:41 PM Revision 4103187a (cdmlib): ref #5458 Added find-by-titleCache method for taxon node service
Patrick Plitzner
03:50 PM Revision f9517a12 (cdm-vaadin): ref #5458 Add taxon filter to distribution settings
Patrick Plitzner
02:17 PM feature request #5970: Implement allowOverride in CdmPreference
Katja Luther wrote:
> we also need to update the databases, do you have to include it into your update script alread...
Andreas Müller
01:04 PM feature request #5970 (Feedback): Implement allowOverride in CdmPreference
we also need to update the databases, do you have to include it into your update script already? Katja Luther
02:00 PM Revision 4a72ff97 (cdm-vaadin): ref #5458 Improve performance for taxon tree in settings dialog
- more efficient caching Patrick Plitzner
01:31 PM bug #5800 (Resolved): Remove "Taxonomically Included In" from list of concept relationship types
Applied in changeset commit:taxeditor|a368dac3747c8f43872f78f3ef83bd7ac69007d3. Katja Luther
01:31 PM Revision a368dac3 (taxeditor): fix #5800: remove taxonomically included from menu
Katja Luther
01:17 PM bug #5870 (Resolved): NPE when trying to open a synonym (or taxon) that has been deleted
This is already solved, the message is that the cdm entity could not be found in the database Katja Luther
01:06 PM feature request #5971 (In Progress): Implement database wide CdmPreference writing
Now it is implemented on editor side, we need the update of the CdmPreference table (allowOverride) to complete it (s... Katja Luther
01:03 PM Revision 9d8df0cf (taxeditor): ref #5971: don't allow to edit local nomenclatural code if allowO...
Katja Luther
12:41 PM Revision b7bfcde7 (taxeditor): ref #5971: minor
Katja Luther
12:16 PM Revision be140ab3 (taxeditor): ref #5971: add an admin page to the prefs and add cdm pref nomencl...
Katja Luther
10:02 AM bug #5660 (Closed): Rename Name Relationship to Name Relationships in Name Details View
close this ticket because it does not need a review. Katja Luther
10:01 AM bug #5660 (Resolved): Rename Name Relationship to Name Relationships in Name Details View
Applied in changeset commit:taxeditor|62d710d7f41510465bbfe9f1c82bcf0ac86b3d7a. Katja Luther
10:01 AM Revision 62d710d7 (taxeditor): fix #5660: rename Name Relationship to Name Relationships
Katja Luther

10/31/2016

04:46 PM bug #5693 (Resolved): Deleting a synonym only deletes the synonym relation
I need to check this also against the new synonym implementation in CDM model. Andreas Müller
04:41 PM bug #6160 (Feedback): Add preservation method and stage as sub class to DefinedTerm
Andreas Müller
04:40 PM bug #6160: Add preservation method and stage as sub class to DefinedTerm
I do not understand this. Classes are not meant to distinguish semantics of defined terms. This is what TermType enum... Andreas Müller
 

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